Parasitic castration of bivalves by trematodes is common, and may significantly reduce the reproductive capacity of ecologically important species. Understanding the intensity of infection is desirable, as it can indicate the time that has passed since infection, and influence the host's physiological and reproductive response. In addition, it is useful to know the developmental stage of the trematode, to understand trematode population trends and reproductive success. However, most existing methods (e.g. visually estimating the degree of infection) to assess intensity are approximate only and not reproducible. Here, we present a method to accurately quantify the percentage of bivalve gonad filled with digenean trematode tissue, based on small squashes of gonad tissue rapidly photographed under light microscopy. A maximum of 15 photographs is required to determine the percentage of the whole gonad occupied by trematodes with a minimum of 90% confidence, with smaller mussels requiring fewer. In addition, the stage of trematode infection can be assessed because full sporocysts, spent sporocysts and free cercariae are clearly distinguishable. Although variation exists in the distribution of trematodes in gonad tissue, and thus in the estimate of percentage of the gonad filled with trematodes, this method represents a marked improvement on current coarse assessments of infection which typically focus on binary presence/absence measures. This technique can be used to facilitate a more sophisticated understanding of host–parasite interactions in bivalves, and can inform the conservation and reproductive biology of environmentally crucial species.